Last modified by lzehl on 2021/07/02 17:06
From version 6.1
edited by lzehl
on 2021/02/18 17:38
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To version 23.3
edited by oschmid
on 2021/02/23 16:21
Change comment: There is no comment for this version

Summary

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1 -XWiki.lzehl
1 +XWiki.oschmid
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4 4  The openMINDS metadata models all consist of modular connectable metadata schemas. Each schema can be referenced by it's type and defines properties (including their expected value) for a set of related metadata.
5 5  
6 6  (% style="text-align: justify;" %)
7 -Please find the HTML description for all schemas of each openMINDS metadata model in the corresponding sub-pages. A short overview for each openMINDS metadata model can be found below.
7 +A short overview for each openMINDS metadata model can be found below, including links to full HTML descriptions for all schemas and links to available metadata instances for selected schemas.
8 8  
9 9  (% style="text-align: justify;" %)
10 10  Note that all metadata models are licensed under the MIT license.
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12 12  
13 13  === openMINDS core ===
14 14  
15 -The openMINDS core metadata model contains schemas that can be used to describe the general origin, resource location, and content of research products in the field of neuroscience. Currently this metadata model comprises 37 usable schemas:
15 +(% style="text-align: justify;" %)
16 +The openMINDS core metadata model contains schemas that can be used to describe the general origin, resource location, and content of research products in the field of neuroscience. Currently ( Feb 2021) this metadata model comprises 37 usable schemas, grouped into five classes:
16 16  
17 -* Affiliation
18 -* ContactInformation
19 -* Contribution
20 -* Organization
21 -* Person
22 -* ContentType
23 -* Copyright
24 -* FileBundle
25 -* FileInstance
26 -* FileRepository
27 -* Hash
28 -* License
29 -* DigitalIdentifier
30 -* DigitalIdentifierSchema
31 -* Funding
32 -* QuantitativeValue
33 -* QuantitativeValueRange
34 -* Dataset
35 -* DatasetVersion
36 -* MetaDataModel
37 -* MetaDataModelVersion
38 -* Model
39 -* ModelVersion
40 -* Project
41 -* Software
42 -* SoftwareVersion
43 -* ParameterSetting
44 -* Protocol
45 -* ProtocolExecution
46 -* Subject
47 -* SubjectGroup
48 -* SubjectGroupState
49 -* SubjectState
50 -* TissueSample
51 -* TissueSampleCollection
52 -* TissueSampleCollectionState
53 -* TissueSampleState
18 +{{html}}
19 + <iframe src="https://humanbrainproject.github.io/openMINDS/core.html" width="100%" style="border:0; height:20em"/>
20 +{{/html}}
54 54  
22 +(% style="text-align: right;" %)
23 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
24 +
25 +{{container layoutStyle="columns"}}
26 +(((
27 +(% class="small" %)
28 +**ACTORS**
29 +Affiliation
30 +ContactInformation
31 +Contribution
32 +Organization
33 +Person
34 +(% class="small" %)
35 +**DATA**
36 +ContentType*
37 +Copyright
38 +FileBundle
39 +FileInstance
40 +FileRepository
41 +Hash
42 +License*
43 +)))
44 +(((
45 +(% class="small" %)
46 +**MISCELLANEOUS**
47 +DigitalIdentifier
48 +DigitalIdentifierSchema*
49 +Funding
50 +QuantitativeValue
51 +QuantitativeValueRange
52 +(% class="small" %)
53 +**PRODUCTS**
54 +Dataset
55 +DatasetVersion
56 +MetaDataModel
57 +MetaDataModelVersion
58 +Model
59 +ModelVersion
60 +Project
61 +Software
62 +SoftwareVersion
63 +)))
64 +(((
65 +(% class="small" %)
66 +**RESEARCH**
67 +ParameterSetting
68 +Protocol
69 +ProtocolExecution
70 +Subject
71 +SubjectGroup
72 +SubjectGroupState
73 +SubjectState
74 +TissueSample
75 +TissueSampleCollection
76 +TissueSampleCollectionState
77 +TissueSampleState
78 +)))
79 +{{/container}}
80 +
81 +(% class="wikigeneratedid" style="text-align: justify;" %)
82 +In case of EBRAINS, metadata representations (instances) of the schemas marked with an asterisk are centrally defined and maintained on a separate GitHub to guarantee more consistency across the database instances of the Knowledge Graph (cf. section openMINDS instances).
83 +
84 +(% class="wikigeneratedid" style="text-align: justify;" %)
85 +For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
86 +
87 +(% class="wikigeneratedid" %)
88 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_core>>https://github.com/HumanBrainProject/openMINDS_core||rel="noopener noreferrer" target="_blank"]]
89 +
55 55  === openMINDS SANDS ===
56 56  
57 -xxx
92 +(% style="text-align: justify;" %)
93 +The openMINDS SANDS (**S**patial **A**nchoring for **N**euroscience **D**ata **S**tructures) metadata model contains schemas that can be used to capture the anatomical location of neuroscience data as well as to identify and highlight commonly used reference brain atlases and coordinate spaces. Currently (Feb 2021) this metadata model comprises 12 metadata schemas:
58 58  
59 -=== openMINDS controlledTerms ===
95 +(% style="text-align: right;" %)
96 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
60 60  
61 -xxx
98 +{{container layoutStyle="columns"}}
99 +(((
100 +(% class="small" %)
101 +AnatomicalEntity
102 +AnatomicalEntityRelation
103 +Annotation
104 +AtlasTerminology
105 +)))
106 +(((
107 +(% class="small" %)
108 +BrainAtlas
109 +BrainAtlasVersion
110 +CoordinatePoint
111 +CoordinateSpace
112 +)))
113 +(((
114 +(% class="small" %)
115 +Electrode
116 +ElectrodeArray
117 +ElectrodeContact
118 +Image
119 +)))
120 +{{/container}}
62 62  
122 +(% class="wikigeneratedid" style="text-align: justify;" %)
123 +For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
124 +
125 +(% class="wikigeneratedid" %)
126 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_SANDS>>https://github.com/HumanBrainProject/openMINDS_SANDS]]
127 +
128 +=== openMINDS controlledTerms - schemas ===
129 +
130 +(% style="text-align: justify;" %)
131 +The openMINDS controlledTerms metadata model contains schemas that ensure consistent registration of well-defined terms, including linkages to existing ontological terms where applicable. Currently (Feb 2021) this metadata model comprises 38 nearly identical schemas:
132 +
133 +(% style="text-align: right;" %)
134 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its full HTML description.
135 +
136 +{{container layoutStyle="columns"}}
137 +(((
138 +(% class="small" %)
139 +AgeCategory
140 +AnatomicalAxesOrientation
141 +BehavioralTask
142 +BiologicalSex
143 +CellType
144 +ContributionType
145 +CriteriaQualityType
146 +DatasetType
147 +Disease
148 +DiseaseModel
149 +EthicsAssessment
150 +FileBundleGrouping
151 +FileUsageRole
152 +)))
153 +(((
154 +(% class="small" %)
155 +Genotype
156 +Language
157 +Laterality
158 +MetaDataModelType
159 +Modality
160 +ModelAbstractionLevel
161 +ModelScope
162 +OperatingDevice
163 +OperatingSystem
164 +Organ
165 +Phenotype
166 +PreparationType
167 +ProductAccessibility
168 +)))
169 +(((
170 +(% class="small" %)
171 +ProgrammingLanguage
172 +QualitativeOverlap
173 +SoftwareApplicationCategory
174 +SoftwareFeature
175 +Species
176 +Strain
177 +Technique
178 +TermSuggestion*
179 +Terminology
180 +TissueSampleType
181 +TypeOfUncertainty
182 +UnitOfMeasurement
183 +)))
184 +{{/container}}
185 +
186 +(% style="text-align: justify;" %)
187 +Except for TermSuggestion (marked with an asterisk), the openMINDS controlledTerms metadata schemas differ only in their type which defines the name of the terminology the correspondingly controlled terms are registered to (cf. openMINDS controlledTerms - terminologies).
188 +
189 +(% style="text-align: justify;" %)
190 +Compared to these schemas, the TermSuggestion has one additional property ("terminology") where users can state to which terminology the new suggested (not yet controlled) term belongs to. Within the EBRAINS Knowledge Graph, the metadata representations for TermSuggestion will be regularly reviewed by the openMINDS development team in order to integrate these community driven suggestions into the controlledTerms terminologies and corresponding ontology (where applicable).
191 +
192 +(% class="wikigeneratedid" style="text-align: justify;" %)
193 +For details, contributing or reviewing examples please checkout as well the corresponding GitHub repository:
194 +
195 +(% class="wikigeneratedid" %)
196 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_controlledTerms>>https://github.com/HumanBrainProject/openMINDS_controlledTerms]]
197 +
198 +=== openMINDS controlledTerms - terminologies ===
199 +
200 +The openMINDS instances repository holds a collection of metadata representations (instances) of selected schemas which content should be more controlled to ensure their consistent definition and usage for the entire EBRAINS Knowledge Graph. Currently the repository holds collections for the following schemas:
201 +
202 +(% style="text-align: right;" %)
203 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
204 +
205 +{{container layoutStyle="columns"}}
206 +(((
207 +(% class="small" %)
208 +AgeCategory
209 +AnatomicalAxesOrientation
210 +BehavioralTask
211 +BiologicalSex
212 +CellType
213 +ContributionType
214 +CriteriaQualityType
215 +DatasetType
216 +Disease
217 +DiseaseModel
218 +EthicsAssessment
219 +FileBundleGrouping
220 +FileUsageRole
221 +)))
222 +(((
223 +(% class="small" %)
224 +Genotype
225 +Language
226 +Laterality
227 +MetaDataModelType
228 +Modality
229 +ModelAbstractionLevel
230 +ModelScope
231 +OperatingDevice
232 +OperatingSystem
233 +Organ
234 +Phenotype
235 +PreparationType
236 +ProductAccessibility
237 +)))
238 +(((
239 +(% class="small" %)
240 +ProgrammingLanguage
241 +QualitativeOverlap
242 +SoftwareApplicationCategory
243 +SoftwareFeature
244 +Species
245 +Strain
246 +Technique
247 +Terminology
248 +TissueSampleType
249 +TypeOfUncertainty
250 +UnitOfMeasurement
251 +)))
252 +{{/container}}
253 +
63 63  === openMINDS instances ===
64 64  
65 -xxx
256 +The openMINDS instances repository holds a collection of metadata representations (instances) of selected schemas which content should be more controlled to ensure their consistent definition and usage for the entire EBRAINS Knowledge Graph. Currently the repository holds collections for the following schemas:
257 +
258 +(% style="text-align: right;" %)
259 +(% class="small" style="color:#7f8c8d" %)Click on a schema to discover its available instances (including their Knowledge Graph ID).
260 +
261 +{{container layoutStyle="columns"}}
262 +(((
263 +(% class="small" %)
264 +contentType
265 +)))
266 +(((
267 +(% class="small" %)
268 +License
269 +)))
270 +(((
271 +(% class="small" %)
272 +DigitalIdentifierSchema
273 +)))
274 +{{/container}}
275 +
276 +(% class="wikigeneratedid" style="text-align: justify;" %)
277 +For details, contributing or reviewing the openMINDS instances please checkout as well the corresponding GitHub repository:
278 +
279 +(% class="wikigeneratedid" %)
280 +[[https:~~/~~/github.com/HumanBrainProject/openMINDS_instances>>https://github.com/HumanBrainProject/openMINDS_instances]]
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openMINDS